Obviously, there is no "index.php" folder or page on the site. I've seen this on a few other implementations I've done, and have never been able to figure it out. But since it varies from machine to machine, I have no choice but to think this is some sort of PHP or Apache configuration issue. I have mod_rewrite enabled. What is the issue here?

A url like http://www.mysite.com/index.php/about-us/ would mean that mod_rewrite has not been detected or is not enabled. Could you post the content of your .htaccess file. Is this a new site or an existing site thats suddenly doing this?

Yes, it does seem like a mod_rewrite issue. I never changed my .htaccess file (I think it's pretty much canned SS), but I DID move from Wampserver to my default Apache/PHP install for serving the site(s) [it's happening on All the sites]. I'm running Apache 2.0.63 and PHP 5.2.5. Below is my .htaccess code:

Sorry to revive an old thread but I wanted to post my solution as this has bugged me twice before, but this third time I could not fix it and had to settle for a workaround.

I could not simply set the base url to a forwardslash as my applications are developed in subfolders and then uploaded to a root directory on the server, I really did not want to compromise the convenience of this.

I simply added this to the main config.php to remove index.php from the baseURL all together.